/*=========================================================================

  Program:   Insight Segmentation & Registration Toolkit
  Module:    $HeadURL$
  Language:  C++
  Date:      $Date$
  Version:   $Revision$

  Copyright (c) Insight Software Consortium. All rights reserved.
  See ITKCopyright.txt or https://www.itk.org/HTML/Copyright.htm for details.

     This software is distributed WITHOUT ANY WARRANTY; without even
     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
     PURPOSE.  See the above copyright notices for more information.

=========================================================================*/
#if defined(_MSC_VER)
# pragma warning(disable : 4786)
#endif

#include "TestGridTransformRegistrationCLP.h"

#include "itkOrientImageFilter.h"
#include "itkResampleImageFilter.h"

#include "itkImageFileWriter.h"

#include "itkPluginUtilities.h"

#include "itkTimeProbesCollectorBase.h"

// Use an anonymous namespace to keep class types and function names
// from colliding when module is used as shared object module.  Every
// thing should be in an anonymous namespace except for the module
// entry point, e.g. main()
//
namespace
{

template <class T>
int DoIt(int argc, char* argv[], T)
{
  PARSE_ARGS;

  // typedefs
  const unsigned int ImageDimension = 3;
  typedef T PixelType;
  typedef itk::Image<PixelType, ImageDimension> InputImageType;

  typedef itk::ImageFileReader<InputImageType> FixedImageReaderType;
  typedef itk::ImageFileReader<InputImageType> MovingImageReaderType;

  typedef itk::VectorImage<double, ImageDimension> GridType;

  GridType::Pointer grid = GridType::New();

  // Set up the grid volume
  {
    grid->SetVectorLength(ImageDimension);

    GridType::IndexType start;

    start[0] = 0;
    start[1] = 0;
    start[2] = 0;

    GridType::SizeType size;

    size[0] = gridSize;
    size[1] = gridSize;
    size[2] = gridSize;

    GridType::RegionType region;
    region.SetSize(size);
    region.SetIndex(start);

    grid->SetRegions(region);
  }

  // Read fixed and moving images
  //
  //
  typename FixedImageReaderType::Pointer fixedImageReader = FixedImageReaderType::New();
  typename MovingImageReaderType::Pointer movingImageReader = MovingImageReaderType::New();

  fixedImageReader->SetFileName(FixedImageFileName.c_str());
  movingImageReader->SetFileName(MovingImageFileName.c_str());

  // Add a time probe
  itk::TimeProbesCollectorBase collector;

  collector.Start("Read fixed volume");
  fixedImageReader->Update();
  collector.Stop("Read fixed volume");

  collector.Start("Read moving volume");
  movingImageReader->Update();
  collector.Stop("Read moving volume");

  collector.Start("Constructing deformation field");
  grid->SetOrigin(fixedImageReader->GetOutput()->GetOrigin());

  // Set the spacing of the grid so that there are the gridSize grid
  // points span the image dimensions.
  GridType::SpacingType spacing = fixedImageReader->GetOutput()->GetSpacing();

  typename InputImageType::RegionType fixedRegion = fixedImageReader->GetOutput()->GetLargestPossibleRegion();
  typename InputImageType::SizeType fixedImageSize = fixedRegion.GetSize();
  for (unsigned int r = 0; r < ImageDimension; r++)
  {
    spacing[r] *= floor(static_cast<double>(fixedImageSize[r] - 1) / static_cast<double>(gridSize - 1));
  }

  grid->SetSpacing(spacing);

  grid->Allocate();

  // Fill with zero
  GridType::PixelContainer* pixelContainer = grid->GetPixelContainer();
  std::fill(pixelContainer->GetBufferPointer(), pixelContainer->GetBufferPointer() + pixelContainer->Size(), 0.0);

  // Set some elements to non-zero
  {
    GridType::IndexType index;
    index[1] = gridSize / 2;
    index[2] = gridSize / 2;

    // Deform by 6 pixels in the x direction
    GridType::PixelType p(3);
    p[0] = 6;
    p[1] = 0;
    p[2] = 0;
    for (int x = 0; x < gridSize; ++x)
    {
      index[0] = x;
      grid->SetPixel(index, p);
    }
  }

  if (OutputTransform != "")
  {
    typedef itk::ImageFileWriter<GridType> GridWriterType;

    GridWriterType::Pointer gridWriter = GridWriterType::New();
    gridWriter->SetFileName(OutputTransform);
    gridWriter->SetInput(grid);

    try
    {
      gridWriter->Update();
    }
    catch (itk::ExceptionObject& exp)
    {
      std::cerr << "Exception caught !" << std::endl;
      std::cerr << exp << std::endl;
    }
  }

  collector.Stop("Constructing deformation field");

  // Report the time taken by the registration
  collector.Report();

  return EXIT_SUCCESS;
}

} // end of anonymous namespace

int main(int argc, char* argv[])
{

  // Print out the arguments (need to add --echo to the argument list
  //
  std::vector<char*> vargsNew;
  for (int vi = 0; vi < argc; ++vi)
  {
    vargsNew.push_back(argv[vi]);
  }
  vargsNew.push_back(const_cast<char*>("--echo"));

  argc = vargsNew.size();
  argv = &(vargsNew[0]);

  PARSE_ARGS;

  itk::IOPixelEnum pixelType;
  itk::IOComponentEnum componentType;

  try
  {
    itk::GetImageType(FixedImageFileName, pixelType, componentType);

    // This filter handles all types

    switch (componentType)
    {
      case itk::IOComponentEnum::CHAR:
      case itk::IOComponentEnum::UCHAR:
      case itk::IOComponentEnum::USHORT:
      case itk::IOComponentEnum::SHORT: return DoIt(argc, argv, static_cast<short>(0)); break;
      case itk::IOComponentEnum::ULONG:
      case itk::IOComponentEnum::LONG:
      case itk::IOComponentEnum::UINT:
      case itk::IOComponentEnum::INT:
      case itk::IOComponentEnum::DOUBLE:
      case itk::IOComponentEnum::FLOAT: return DoIt(argc, argv, static_cast<float>(0)); break;
      case itk::IOComponentEnum::UNKNOWNCOMPONENTTYPE:
      default: std::cout << "unknown component type" << std::endl; break;
    }
  }
  catch (itk::ExceptionObject& excep)
  {
    std::cerr << argv[0] << ": exception caught !" << std::endl;
    std::cerr << excep << std::endl;
    return EXIT_FAILURE;
  }
  return EXIT_SUCCESS;
}
